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Vela J, Mora P, Montiel EE, Rico-Porras JM, Sanllorente O, Amoasii D, Lorite P, Palomeque T. Exploring horizontal transfer of mariner transposable elements among ants and aphids. Gene 2024; 899:148144. [PMID: 38195050 DOI: 10.1016/j.gene.2024.148144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/11/2024]
Abstract
Aphids and ants are mutualistic species with a close space-time relationship, which may facilitate the occurrence of horizontal transfer events between these insect groups. Myrmar-like mariner elements were previously isolated from two ant (Myrmica ruginodis and Tapinoma ibericum) and two aphid species (Aphis fabae and Aphis hederae). The aim of this work is to determine the presence of Myrmar-like mariner elements in new ant and aphid species, as well as to analyze the likelihood of horizontal transfer events between these taxa. To accomplish this, the Myrmar-like element has been isolated from five aphid species and six ant species. Among these new analyzed species, full-length Myrmar-like mariner elements with very high sequence similarity have been isolated from the aphids Aphis nerii, Aphis spiraecola, Brachycaudus cardui, and Rhopalosiphum maidis as well as from the ants Lasius grandis and Lasius niger, even though aphids and ants belong to two insect orders (Hemiptera and Hymenoptera) that have evolved independently for at least 300 million-years. Both Lasius species establish frequent mutualistic relationships with multiple aphid species, including A. nerii, A. spiraecola, and B. cardui. The study of the putative protein encoded by them and the phylogenetic analysis suggests that they could be active transposons shared by aphids and ants through horizontal transfer events. Additionally, mariner elements with internal deletion were found in several aphids and one ant species, showing a high degree of sequence similarity among them. The characteristics of these elements with internal deletion suggest a complex origin involving various evolutionary processes, possibly including also horizontal transfer events. Myrmar-like elements have also been isolated from the other ant species, although without similarity with the aphid mariner sequences. Myrmar-like elements are also present in phylogenetically distant insect species, as well as in one crustacean species. The phylogenetic study carried out with all Myrmar-like elements suggests the probable occurrence of horizontal transfer events.
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Affiliation(s)
- Jesús Vela
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Pablo Mora
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Eugenia E Montiel
- Departamento de Biología (Genética), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain; Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | - José M Rico-Porras
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Olivia Sanllorente
- Departamento de Zoología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| | - Daniela Amoasii
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
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Aubin E, El Baidouri M, Panaud O. Horizontal Gene Transfers in Plants. Life (Basel) 2021; 11:life11080857. [PMID: 34440601 PMCID: PMC8401529 DOI: 10.3390/life11080857] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 12/24/2022] Open
Abstract
In plants, as in all eukaryotes, the vertical transmission of genetic information through reproduction ensures the maintenance of the integrity of species. However, many reports over the past few years have clearly shown that horizontal gene transfers, referred to as HGTs (the interspecific transmission of genetic information across reproductive barriers) are very common in nature and concern all living organisms including plants. The advent of next-generation sequencing technologies (NGS) has opened new perspectives for the study of HGTs through comparative genomic approaches. In this review, we provide an up-to-date view of our current knowledge of HGTs in plants.
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Shen E, Chen T, Zhu X, Fan L, Sun J, Llewellyn DJ, Wilson I, Zhu QH. Expansion of MIR482/2118 by a class-II transposable element in cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:2084-2099. [PMID: 32578284 DOI: 10.1111/tpj.14885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 05/28/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
Some plant microRNA (miRNA) families contain multiple members generating identical or highly similar mature miRNA variants. Mechanisms underlying the expansion of miRNA families remain elusive, although tandem and/or segmental duplications have been proposed. In this study of two tetraploid cottons, Gossypium hirsutum and Gossypium barbadense, and their extant diploid progenitors, Gossypium arboreum and Gossypium raimondii, we investigated the gain and loss of members of the miR482/2118 superfamily, which modulates the expression of nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance genes. We found significant expansion of MIR482/2118d in G. barbadense, G. hirsutum and G. raimondii, but not in G. arboreum. Several newly expanded MIR482/2118d loci have mutated to produce different miR482/2118 variants with altered target-gene specificity. Based on detailed analysis of sequences flanking these MIR482/2118 loci, we found that this expansion of MIR482/2118d and its derivatives resulted from an initial capture of an MIR482/2118d by a class-II DNA transposable element (TE) in G. raimondii prior to the tetraploidization event, followed by transposition to new genomic locations in G. barbadense, G. hirsutum and G. raimondii. The 'GosTE' involved in the capture and proliferation of MIR482/2118d and its derivatives belongs to the PIF/Harbinger superfamily, generating a 3-bp target site duplication upon insertion at new locations. All orthologous MIR482/2118 loci in the two diploids were retained in the two tetraploids, but mutation(s) in miR482/2118 were observed across all four species as well as in different cultivars of both G. barbadense and G. hirsutum, suggesting a dynamic co-evolution of miR482/2118 and its NBS-LRR targets. Our results provide fresh insights into the mechanisms contributing to MIRNA proliferation and enrich our knowledge on TEs.
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Affiliation(s)
- Enhui Shen
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- New Rural Development Institute, Zhejiang University, Hangzhou, 310058, China
| | - Tianzi Chen
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xintian Zhu
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Longjiang Fan
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jie Sun
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832000, China
| | - Danny J Llewellyn
- Black Mountain Laboratories, CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Iain Wilson
- Black Mountain Laboratories, CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Qian-Hao Zhu
- Black Mountain Laboratories, CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
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Complex Evolutionary History of Mboumar, a Mariner Element Widely Represented in Ant Genomes. Sci Rep 2020; 10:2610. [PMID: 32054918 PMCID: PMC7018970 DOI: 10.1038/s41598-020-59422-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 01/28/2020] [Indexed: 12/21/2022] Open
Abstract
Mboumar-9 is an active mariner-transposable element previously isolated in the ant Messor bouvieri. In this work, a mariner-like element, Mboumar, isolated from 22 species of ants, is analyzed. These species belong to nine different subfamilies, including Leptanillinae, the most primitive ant subfamily, and Myrmicinae and Formicidae, the most derived ones. Consequently, Mboumar-like elements seem to be well-represented in ant genomes. The phylogenetic tree drawn for mariner elements is highly inconsistent with the phylogeny of host ants, with almost identical elements found in clearly distant species and, on the contrary, more variable elements in closely related species. The inconsistency between the two phylogenetic trees indicates that these transposable elements have evolved independently from the speciation events of the ants that host them. Besides, we found closer genetic relationships among elements than among their host ants. We also found potential coding copies with an uninterrupted open reading frame of 345 aa in 11 species. The putative transposase codified by them showed a high sequence identity with the active Mboumar-9 transposase. The results of selection tests suggest the intervention of purifying selection in the evolution of these elements. Overall, our study suggests a complex evolutionary history of the Mboumar-like mariner in ants, with important participation of horizontal transfer events. We also suggest that the evolutionary dynamics of Mboumar-like elements can be influenced by the genetic system of their host ants, which are eusocial insects with a haplodiploid genetic system.
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Divashuk MG, Karlov GI, Kroupin PY. Copy Number Variation of Transposable Elements in Thinopyrum intermedium and Its Diploid Relative Species. PLANTS (BASEL, SWITZERLAND) 2019; 9:E15. [PMID: 31877707 PMCID: PMC7020174 DOI: 10.3390/plants9010015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/05/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022]
Abstract
Diploid and polyploid wild species of Triticeae have complex relationships, and the understanding of their evolution and speciation could help to increase the usability of them in wheat breeding as a source of genetic diversity. The diploid species Pseudoroegneria spicata (St), Thinopyrum bessarabicum (Jb), Dasypyrum villosum (V) derived from a hypothetical common ancestor are considered to be possible subgenome donors in hexaploid species Th. intermedium (JrJvsSt, where indices r, v, and s stand for the partial relation to the genomes of Secale, Dasypyrum, and Pseudoroegneria, respectively). We quantified 10 families of transposable elements (TEs) in P. spicata, Th. bessarabicum, D. villosum (per one genome), and Th. intermedium (per one average subgenome) using the quantitative real time PCR assay and compared their abundance within the studied genomes as well as between them. Sabrina was the most abundant among all studied elements in P. spicata, D. villosum, and Th. intermedium, and among Ty3/Gypsy elements in all studied species. Among Ty1/Copia elements, Angela-A and WIS-A showed the highest and close abundance with the exception of D. villosum, and comprised the majority of all studied elements in Th. bessarabicum. Sabrina, BAGY2, and Angela-A showed similar abundance among diploids and in Th. intermedium hexaploid; Latidu and Barbara demonstrated sharp differences between diploid genomes. The relationships between genomes of Triticeae species based on the studied TE abundance and the role of TEs in speciation and polyploidization in the light of the current phylogenetic models is discussed.
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Affiliation(s)
- Mikhail G. Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (M.G.D.)
- Centre for Molecular Biotechnology, Russian State Agrarian University-Timiryazev Agricultural Academy, Moscow 127550, Russia
| | - Gennady I. Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (M.G.D.)
- Centre for Molecular Biotechnology, Russian State Agrarian University-Timiryazev Agricultural Academy, Moscow 127550, Russia
| | - Pavel Yu. Kroupin
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (M.G.D.)
- Centre for Molecular Biotechnology, Russian State Agrarian University-Timiryazev Agricultural Academy, Moscow 127550, Russia
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Hsu CC, Lai PH, Chen TC, Tsai WC, Hsu JL, Hsiao YY, Wu WL, Tsai CH, Chen WH, Chen HH. PePIF1, a P-lineage of PIF-like transposable element identified in protocorm-like bodies of Phalaenopsis orchids. BMC Genomics 2019; 20:25. [PMID: 30626325 PMCID: PMC6327408 DOI: 10.1186/s12864-018-5420-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 12/27/2018] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Orchids produce a colorless protocorm by symbiosis with fungi upon seed germination. For mass production of orchids, the prevailing approaches are both generation of protocorm-like bodies (PLBs) from callus and multiplication of adventitious buds on inflorescence. However, somaclonal variations occur during micropropagation. RESULTS We isolated the two most expressed transposable elements belonging to P Instability Factor (PIF)-like transposons. Among them, a potential autonomous element was identified by similarity analysis against the whole-genome sequence of Phalaenopsis equestris and named PePIF1. It contains a 19-bp terminal inverted repeat flanked by a 3-bp target site duplication and two coding regions encoding ORF1- and transposase-like proteins. Phylogenetic analysis revealed that PePIF1 belongs to a new P-lineage of PIF. Furthermore, two distinct families, PePIF1a and PePIF1b, with 29 and 37 putative autonomous elements, respectively, were isolated, along with more than 3000 non-autonomous and miniature inverted-repeat transposable element (MITE)-like elements. Among them, 828 PePIF1-related elements were inserted in 771 predicted genes. Intriguingly, PePIF1 was transposed in the somaclonal variants of Phalaenopsis cultivars, as revealed by transposon display, and the newly inserted genes were identified and sequenced. CONCLUSION A PIF-like element, PePIF1, was identified in the Phalaenopsis genome and actively transposed during micropropagation. With the identification of PePIF1, we have more understanding of the Phalaenopsis genome structure and somaclonal variations during micropropagation for use in orchid breeding and production.
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Affiliation(s)
- Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Han Lai
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Tien-Chih Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Chung Hsing University, Tainan, Taiwan
| | - Jui-Lin Hsu
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Luan Wu
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Huei Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
| | - Hong-Hwa Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- Institute of Tropical Plant Sciences, National Chung Hsing University, Tainan, Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
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Markova DN, Mason-Gamer RJ. Transcriptional activity of PIF and Pong-like Class II transposable elements in Triticeae. BMC Evol Biol 2017; 17:178. [PMID: 28774284 PMCID: PMC5543537 DOI: 10.1186/s12862-017-1028-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 07/26/2017] [Indexed: 11/10/2022] Open
Abstract
Background Transposable elements are major contributors to genome size and variability, accounting for approximately 70–80% of the maize, barley, and wheat genomes. PIF and Pong-like elements belong to two closely-related element families within the PIF/Harbinger superfamily of Class II (DNA) transposons. Both elements contain two open reading frames; one encodes a transposase (ORF2) that catalyzes transposition of the functional elements and their related non-autonomous elements, while the function of the second is still debated. In this work, we surveyed for PIF- and Pong-related transcriptional activity in 13 diploid Triticeae species, all of which have been previously shown to harbor extensive within-genome diversity of both groups of elements. Results The results revealed that PIF elements have considerable transcriptional activity in Triticeae, suggesting that they can escape the initial levels of plant cell control and are regulated at the post-transcriptional level. Phylogenetic analysis of 156 PIF cDNA transposase fragments along with 240 genomic partial transposase sequences showed that most, if not all, PIF clades are transcriptionally competent, and that multiple transposases coexisting within a single genome have the potential to act simultaneously. In contrast, we did not detect any transcriptional activity of Pong elements in any sample. Conclusions The lack of Pong element transcription shows that even closely related transposon families can exhibit wide variation in their transposase transcriptional activity within the same genome. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1028-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dragomira N Markova
- Department of Biological Sciences, University of Illinois at Chicago, M/C 067 840 West Taylor Street, Chicago, IL, 60607, USA. .,Present address: Department of Plant Sciences (mail stop 3), 151 Asmundson Hall, University of California, Davis, CA, 95616, USA.
| | - Roberta J Mason-Gamer
- Department of Biological Sciences, University of Illinois at Chicago, M/C 067 840 West Taylor Street, Chicago, IL, 60607, USA
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Mahelka V, Krak K, Kopecký D, Fehrer J, Šafář J, Bartoš J, Hobza R, Blavet N, Blattner FR. Multiple horizontal transfers of nuclear ribosomal genes between phylogenetically distinct grass lineages. Proc Natl Acad Sci U S A 2017; 114:1726-1731. [PMID: 28137844 PMCID: PMC5320982 DOI: 10.1073/pnas.1613375114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The movement of nuclear DNA from one vascular plant species to another in the absence of fertilization is thought to be rare. Here, nonnative rRNA gene [ribosomal DNA (rDNA)] copies were identified in a set of 16 diploid barley (Hordeum) species; their origin was traceable via their internal transcribed spacer (ITS) sequence to five distinct Panicoideae genera, a lineage that split from the Pooideae about 60 Mya. Phylogenetic, cytogenetic, and genomic analyses implied that the nonnative sequences were acquired between 1 and 5 Mya after a series of multiple events, with the result that some current Hordeum sp. individuals harbor up to five different panicoid rDNA units in addition to the native Hordeum rDNA copies. There was no evidence that any of the nonnative rDNA units were transcribed; some showed indications of having been silenced via pseudogenization. A single copy of a Panicum sp. rDNA unit present in H. bogdanii had been interrupted by a native transposable element and was surrounded by about 70 kbp of mostly noncoding sequence of panicoid origin. The data suggest that horizontal gene transfer between vascular plants is not a rare event, that it is not necessarily restricted to one or a few genes only, and that it can be selectively neutral.
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MESH Headings
- Cell Nucleus/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Diploidy
- Evolution, Molecular
- Gene Transfer, Horizontal
- Genes, Plant/genetics
- Hordeum/classification
- Hordeum/genetics
- Phylogeny
- Poaceae/classification
- Poaceae/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Václav Mahelka
- Institute of Botany, The Czech Academy of Sciences, Průhonice 25243, Czech Republic;
| | - Karol Krak
- Institute of Botany, The Czech Academy of Sciences, Průhonice 25243, Czech Republic
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague 6 16500, Czech Republic
| | - David Kopecký
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Judith Fehrer
- Institute of Botany, The Czech Academy of Sciences, Průhonice 25243, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Jan Bartoš
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Roman Hobza
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
- Institute of Biophysics, The Czech Academy of Sciences, Brno 61265, Czech Republic
| | - Nicolas Blavet
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Frank R Blattner
- Experimental Taxonomy, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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Genetic Engineering and Sustainable Crop Disease Management: Opportunities for Case-by-Case Decision-Making. SUSTAINABILITY 2016. [DOI: 10.3390/su8050495] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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